An evidence-based knowledgebase of metastasis suppressors to identify key pathways relevant to cancer metastasis

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Zhao, Min ^a   Li, Zhe ^b   Qu, Hong ^b  

^a UNIVERSITY OF THE SUNSHINE COAST   (Australia)

^b PEKING UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

TUMOR PROTEIN;

BIOLOGY; BIOSYNTHESIS; CELL PROLIFERATION; EPITHELIUM CELL; GENE EXPRESSION REGULATION; GENETICS; HUMAN; METABOLISM; METASTASIS; MORPHOGENESIS; MUTATION; NEOPLASM; PATHOLOGY; PROCEDURES; SIGNAL TRANSDUCTION;

CELL PROLIFERATION; COMPUTATIONAL BIOLOGY; EPITHELIAL CELLS; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; MORPHOGENESIS; MUTATION; NEOPLASM METASTASIS; NEOPLASM PROTEINS; NEOPLASMS; SIGNAL TRANSDUCTION;

EID: 84944938060     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep15478     Document Type: Article

References (55)

1. Balmain, A., Gray, J. & Ponder, B. The genetics and genomics of cancer. Nat Genet. 33 Suppl, 238-244 (2003).
2. Haber, D. A. & Settleman, J. Cancer: drivers and passengers. Nature 446, 145-146 (2007).
3. Steeg, P. S. et al. Evidence for a novel gene associated with low tumor metastatic potential. J Natl Cancer Inst. 80, 200-204 (1988).
4. Yan, J., Yang, Q. & Huang, Q. Metastasis suppressor genes. Histol Histopathol 28, 285-292 (2013).
5. Stafford, L. J., Vaidya, K. S. & Welch, D. R. Metastasis suppressors genes in cancer. Int J Biochem Cell Biol. 40, 874-891 (2008).
6. Hurst, D. R. & Welch, D. R. Metastasis suppressor genes at the interface between the environment and tumor cell growth. Int Rev Cell Mol Biol. 286, 107-180 (2011).
7. Berger, J. C., Vander Griend, D. J., Robinson, V. L., Hickson, J. A. & Rinker-Schaeffer, C. W. Metastasis suppressor genes: from gene identification to protein function and regulation. Cancer Biol Ther. 4, 805-812 (2005).
8. Pencheva, N. & Tavazoie, S. F. Control of metastatic progression by microRNA regulatory networks. Nat Cell Biol. 15, 546-554 (2013).
9. Network TCGAR. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 1061-1068 (2008).
10. Network TCGAR. Comprehensive molecular characterization of human colon and rectal cancer. Nature 487, 330-337 (2012).
11. Network TCGAR. Integrated genomic analyses of ovarian carcinoma. Nature 474, 609-615 (2011).
12. Verhaak, R. G. et al. Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell 17, 98-110 (2010).
13. Wrzeszczynski, K. O. et al. Identification of tumor suppressors and oncogenes from genomic and epigenetic features in ovarian cancer. PLoS One 6, e28503 (2011).
14. Forbes, S. A. et al. COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer. Nucleic Acids Res. 38, D652-657 (2010).
15. Wu, C. et al. BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol. 10, R130 (2009).
16. Lv, J. et al. DiseaseMeth: a human disease methylation database. Nucleic Acids Res. 40, D1030-1035 (2012).
17. Sayers, E. W. et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 39, D38-51 (2011).
18. Magrane, M. & Consortium, U. UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford) 2011, bar009 (2011).
19. Flicek, P. et al. Ensembl 2011. Nucleic Acids Res. 39, D800-806 (2011).
20. Gene Ontology Consortium. The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 38, D331-335 (2010).
21. Su, A. I. et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA 101, 6062-6067 (2004).
22. Uhlen, M. et al. Proteomics. Tissue-based map of the human proteome. Science 347, 1260419 (2015).
23. Zhao, M., Chen, Y., Qu, D. & Qu, H. TSdb: a database of transporter substrates linking metabolic pathways and transporter systems on a genome scale via their shared substrates. Sci China Life Sci. 54, 60-64 (2011).
24. Karp, P. D. et al. Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res. 33, 6083-6089 (2005).
25. Kanehisa, M. et al. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 36, D480-484 (2008).
26. Zhao, M., Chen, X., Gao, G., Tao, L. & Wei, L. RLEdb: a database of rate-limiting enzymes and their regulation in human, rat, mouse, yeast and E. coli. Cell Res. 19, 793-795 (2009).
27. Thomas, P. D. et al. PANTHER: a library of protein families and subfamilies indexed by function. Genome Res. 13, 2129-2141 (2003).
28. Schaefer, C. F. et al. PID: the Pathway Interaction Database. Nucleic Acids Res. 37, D674-679 (2009).
29. Zhao, M. & Qu, H. PathLocdb: a comprehensive database for the subcellular localization of metabolic pathways and its application to multiple localization analysis. BMC Genomics 11 Suppl 4, S13 (2010).
30. Croft, D. et al. Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res. 39, D691-697 (2011).
31. Matthews, L. et al. Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res. 37, D619-622 (2009).
32. Becker, K. G., Barnes, K. C., Bright, T. J. & Wang, S. A. The genetic association database. Nat Genet. 36, 431-432 (2004).
33. Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M. & Hirakawa, M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 38, D355-360 (2010).
34. Osborne, J. D. et al. Annotating the human genome with Disease Ontology. BMC Genomics 10 Suppl 1, S6 (2009).
35. Du, P. et al. From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations. Bioinformatics 25, i63-68 (2009).
36. Hindorff, L. A. et al. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 106, 9362-9367 (2009).
37. Maglott, D., Ostell, J., Pruitt, K. D. & Tatusova, T. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res. 39, D52-D57 (2011).
38. Kanehisa, M. et al. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34, D354-357 (2006).
39. D. N., BioCarta. Biotech Software & Internet Report 2, 117-120 (2001).
40. Xie, C. et al. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res. 39, W316-322 (2011).
41. Chen, J., Bardes, E. E., Aronow, B. J. & Jegga, A. G. ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Res. 37, W305-311 (2009).
42. Gao, J. et al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal 6, pl1 (2013).
43. Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature 474, 609-615 (2011).
44. Zhao, M., Sun, J. & Zhao, Z. Distinct and competitive regulatory patterns of tumor suppressor genes and oncogenes in ovarian cancer. PLoS One 7, e44175 (2012).
45. Zhao, M., Sun, J. & Zhao, Z. Synergetic regulatory networks mediated by oncogene-driven microRNAs and transcription factors in serous ovarian cancer. Mol Biosyst 9, 3187-3198 (2013).
46. Tusher, V. G., Tibshirani, R. & Chu, G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 98, 5116-5121 (2001).
47. Gao, D., Vahdat, L. T., Wong, S., Chang, J. C. & Mittal, V. Microenvironmental regulation of epithelial-mesenchymal transitions in cancer. Cancer Res 72, 4883-4889 (2012).
48. Nikitovic, D. et al. The Motile Breast Cancer Phenotype Roles of Proteoglycans/Glycosaminoglycans. BioMed Research International 2014, 13 (2014).
49. Gay, L. J. & Felding-Habermann, B. Contribution of platelets to tumour metastasis. Nat Rev Cancer 11, 123-134 (2011).
50. Su, Z., Yang, Z., Xu, Y., Chen, Y. & Yu, Q. Apoptosis, autophagy, necroptosis, and cancer metastasis. Mol Cancer 14, 48 (2015).
51. Zhao, M., Sun, J. & Zhao, Z. TSGene: a web resource for tumor suppressor genes. Nucleic Acids Res. 41, D970-976 (2013).
52. Bandyopadhyay, S. et al. PTEN up-regulates the tumor metastasis suppressor gene Drg-1 in prostate and breast cancer. Cancer Res. 64, 7655-7660 (2004).
53. Chowdhury, S. et al. Restoration of PTEN activity decreases metastases in an orthotopic model of colon cancer. J Surg Res. 184, 755-760 (2013).
54. Gillan, L. et al. Periostin secreted by epithelial ovarian carcinoma is a ligand for alpha(V)beta(3) and alpha(V)beta(5) integrins and promotes cell motility. Cancer Res. 62, 5358-5364 (2002).
55. Chen, C. et al. Smad4 mediates malignant behaviors of human ovarian carcinoma cell through the effect on expressions of E-cadherin, plasminogen activator inhibitor-1 and VEGF. BMB Rep. 43, 554-560 (2010).